how can i cluster the result in .dcd file using chimera on a superomputer?
Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks
Hi Ibrahim, Sorry, but this is way too hard. That part of Chimera simply was not designed for scripting. ChimeraX is much better at allowing scripting, but it doesn't have the clustering functionality you need. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2020, at 5:05 AM, Ibrahim Mohamed <hollow_ichigo199799@yahoo.com> wrote:
Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
can you provide me, if it is possible, with the script of clustering from dcd file? i am thinking about running the script only on google colab after i upload the files (dcd and psf). Since colab has a larger RAM Maybe it will work. بتاريخ الخميس، 16 تموز 2020 07:04:21 م غرينتش+2، Eric Pettersen <pett@cgl.ucsf.edu> كتب: Hi Ibrahim, Sorry, but this is way too hard. That part of Chimera simply was not designed for scripting. ChimeraX is much better at allowing scripting, but it doesn't have the clustering functionality you need. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 16, 2020, at 5:05 AM, Ibrahim Mohamed <hollow_ichigo199799@yahoo.com> wrote: Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ibrahim, I'm not sure what part of my previous answer was unclear. Writing such a script would be very, very hard because the trajectory reading/analysis code was not designed for scripting. So effectively the answer is no, there is no way to cluster from a DCD using a script with Chimera. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2020, at 10:35 AM, Ibrahim Mohamed <hollow_ichigo199799@yahoo.com> wrote:
can you provide me, if it is possible, with the script of clustering from dcd file? i am thinking about running the script only on google colab after i upload the files (dcd and psf). Since colab has a larger RAM Maybe it will work.
بتاريخ الخميس، 16 تموز 2020 07:04:21 م غرينتش+2، Eric Pettersen <pett@cgl.ucsf.edu> كتب:
Hi Ibrahim, Sorry, but this is way too hard. That part of Chimera simply was not designed for scripting. ChimeraX is much better at allowing scripting, but it doesn't have the clustering functionality you need.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2020, at 5:05 AM, Ibrahim Mohamed <hollow_ichigo199799@yahoo.com <mailto:hollow_ichigo199799@yahoo.com>> wrote:
Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Eric Pettersen -
Ibrahim Mohamed